tag:blogger.com,1999:blog-37148773.post5680752864165079305..comments2018-02-17T19:45:49.280-05:00Comments on <center>Sandwalk</center>: ENCODE's false claims about the number of regulatory sites per geneLaurence A. Moranhttps://plus.google.com/116237327501105508655noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-37148773.post-26519800561117642952018-02-06T15:52:34.324-05:002018-02-06T15:52:34.324-05:00In analogy to a &quot;notpology&quot;, that is a &...In analogy to a &quot;notpology&quot;, that is a &quot;nottraction&quot;.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-23672018230478045132018-02-06T13:34:24.353-05:002018-02-06T13:34:24.353-05:00@lantog I believe you&#39;re thinking of
Defining...@lantog I believe you&#39;re thinking of<br /><br /><a href="http://www.pnas.org/content/111/17/6131" rel="nofollow">Defining functional DNA elements in the human genome</a><br /><br />It&#39;s not a retraction per se, but they definitely seemed to soften their position (especially in comparison to the hype-building interviews that a small number of the ENCODE researchers gave to the media back in 2012) regarding how much of the human genome must be functional. For example:<br /><br />&quot;Thus, unanswered questions related to biological noise, along with differences in the resolution, sensitivity, and activity level of the corresponding assays, help to explain divergent estimates of the portion of the human genome encoding functional elements. Nevertheless, they do not account for the entire gulf between constrained regions and biochemical activity. Our analysis revealed a vast portion of the genome that appears to be evolving neutrally according to our metrics, even though it shows reproducible biochemical activity, which we previously referred to as “biochemically active but selectively neutral” (68). It could be argued that some of these regions are unlikely to serve critical functions, especially those with lower-level biochemical signal. However, we also acknowledge substantial limitations in our current detection of constraint, given that some human-specific functions are essential but not conserved and that disease-relevant regions need not be selectively constrained to be functional. Despite these limitations, all three approaches [genetic, evolutionary, and biochemical - Dave] are needed to complete the unfinished process of inferring functional DNA elements, specifying their boundaries, and defining what functions they serve at molecular, cellular, and organismal levels.&quot;Dave Carlsonhttps://www.blogger.com/profile/18110718908216269032noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-29760018514025909732018-02-06T12:02:22.138-05:002018-02-06T12:02:22.138-05:00I was under the impression that Birney and Stamato...I was under the impression that Birney and Stamatoyannopoulos did issue a retraction of sorts. In a subsequent paper they said that by &#39;function&#39; they didn&#39;t mean what everyone else meant by &#39;function&#39;lantoghttps://lantog.wordpress.com/noreply@blogger.com